The Y chromosome as a tool for studying human evolution Amanda B. Spurdle and Trefor Jenkins MRC Human Ecogenetics Research Unit, South African Institute for Medical Research and University of the Witwatersrand, Johannesburg, South Africa The use of the Y chromosome in human evolutionary research has only recently begun to gain momentum, partly because of a paucity of polymorphism. Differences in male/female behaviour patterns and the unique mode of inheritance of the Y chromosome also complicate interpretation of the data on Y chromosome variation.
Current Opinion in Genetics and Development 1992, 2:487-491
Introduction Scientists have long been fascinated by studies of the origin and more recent evolution of mankind. Paleoanthropological research has led to two opposing theories of origin, popularly known as the 'out of Africa' and multiregional continuum models. The 'out of Africa' hypothesis proposes that modem humans evolved in Africa, and subsequendy dispersed throughout Europe and Asia, replacing all other hominids [1,2oo]. As an extension of this theory, distinction at the genetic level has been implicated in the lack of interbreeding between the archaic humans occupying Europe and Asia, and the invading African ancestor [3]. The multiregional continuum model postulates that modem humans evolved gradually and simultaneously from local forms of H o m o erectus which had themselves spread from Africa to Europe and Asia [4]; the unity of the species is presumed to have been maintained by gene exchange between the isolates. Research in the field of human genetic variation has ushered in a new era in evolutionary research, and various molecular studies have been undertaken in an attempt to resolve uncertainties resulting from different interpretations of paleoanthropological data. These studies range from the pioneering serogenetic [5] and human leukocyte antigen-complex (HLA) [6] studies to DNAbased restriction fragment length polymorphism (RFLP) analysis of beta-globin markers [7], mitochondrial (mt) DNA [1] and nuclear gene markers [8,9,10oo]. More recently, a comprehensive study invoMng DNA sequencing of the mt.DNA D-loop region has been presented [2°°]. The molecular approach to evolutionary studies is based on the assumption that if modem man arose in Africa,
then African and non-African humans would be most geneticaUy distinct, and African populations would exhibit more within-group genetic variation than the non-African populations that stemmed from an African migration. With little exception, the molecular data confirm the African/non-African split, in support of the 'out of Africa' model. Many researchers have recognized the potential of Y chromosome population and evolutionary studies for providing a record of male-specific gene flow and human evolution, and to thus complement or expand studies using mtDNA or nuclear markers. Unfortunately, the role of the Y chromosome in this area has been limited, not by inadequate effort, but by the singular lack of polymorphism discovered on this chromosome to date. These findings are especially troubling since interpopulation variation differences can only be truly evaluated in light of within-group variation, and it will be di/~cult to make progress and to draw accurate conclusions of an evolutionary nature as long as we are limited by the low levels of Y-specific variation. This review describes current findings on the level of Y chromosome polymorphism, and also details results from Y chromosome population/evolutionary studies using several different Y-specific polymorphic loci.
The paucity of Y chromosome polymorphism Several studies have been undertaken to search for conventional RFLPs on theY chromosome [11, 12] (A Spur-
Abbreviations HLA--human leukocyteantigen-complex;Ht--haplotype; rnt--mitochondrial;PFGE~pulsed-fieldgel electrophoresis; RFLP--restrictionfragment length polyrnnorphisrn. (~ Current Biology Ltd ISSN 0959-437X
487
488 Mammaliangenetics die, T Jenkins, unpublished data; M Jobling, personal communication). Despite these systematic searches, a paucity of polymorphism exists, with reported levels of polymorphism as low as < 1/18000 nucleotides [11] and < 1/46515 nucleotides [12]. This lack of variation is not confined to nucleotide changes occurring within restriction endonuclease sites. Studies on two Y-derived CA repeats have not revealed any polymorphism in 20 Caucasian/Asian males (Z Ulinowski, D Bailey, K Taylor, J Wolfe, personal conmmnication). The repeats also appear to occur less frequently, with positive signals for 5% of Y cosmids, as opposed to 20% of cosmids derived from the long arm of chromosome 9 (9q). In addition, sequencing of the Y chromosome has revealed a very low level of nucleotide diversity, although somewhat higher than estimates based on RFLP studies (M Hammer, personal communication). The implication is that many kilobases of each Y chromosome would need to be sequenced to match the information revealed by mtDNA D-loop sequences used in published evolutionary studies [2"']. This dearth of polymorphism is unexpected in view of theories on the origin of the Y chromosome (see [13%14"] for a review). The proto-Y chromosome is believed to have evolved from a homologous proto-X chromosome, and with the exception of the genes involved in sex determination and the present region of homology between the sex chromosomes, was prone to rearrangement processes and loss/inactivation of genes [15,16,17"-19.]. The Y chromosome was presumably also free to accumulate satellite sequences and noncoding retrotransposed elements originating from autosomes, possibly as a response to selection for a chromosome size that would be appropriate for efficient meiotic segregation [18.]. Despite this plethora of non-coding sequences, simple sequence polymorphism is rare, and most of the reported Y-specific polymorphism is generated, at least in part, by rearrangement processes [20-22,23"]. Malaspina et at [12] have proposed several explanations for the low frequency of polymorphism on the Y chromosome. One suggestion is that the mechanisms protecting the Y chromosome from recombination may simultaneously protect it from mutagenesis, but the role of recombination in maintaining genetic variation is considered more important [12]. The latter explanation arises from the postulate by Clark [24] that Y chromosome polymorphism is unlikely to be maintained by natural selection. It is possible that insufficient time has elapsed since the origin of the present-day Y chromosome to allow for the accumulation of significant polymorphism. Indeed, sequencing studies of the pseudoautosomal boundary region [25,26] show that the Y boundary exhibits less variation than the X boundary, suggesting that it has evolved more recently. However, a survey for long-range Y-specific polymorphism using pulsed-field gel electrophoresis (PFGE) has identified several novel hypervariable blocks (M Jobling, personal communication), contrasting with the results from RFLP screening. These findings suggest that such large scale
polymorphism is generated at a higher rate than simple sequence polymorphism.
The value of the Y-specific probes 49a and 49f Y chromosome probes 49a and 49f are different subclones of cosmid 49 [27], and both detect about 15 Y-specific TaqI bands corresponding to a low copy number sequence [28]. At least eight of these bands have been shown to be present, absent or variable in length [22,23",28-31]. Each variable band was originally considered to represent an independent locus, and the TaqI RFLPs were proposed to result from point mutations only [28]. Recent reports of co-inherited 'alleles' of the A, D and F series [22,23.] have led, however, to the realization that duplication processes cannot be excluded as a mechanism for the generation of at least part of the polymorphism. Thus fragments that appear to be identical may not necessarily originate from the same piece of DNA, and in some cases may represent more than one copy of a duplicated 'locus'. In retrospect, the existence of rearrangements should not be unexpected in view of the origin and nature of the repeat sequences detected by 49a/f. The Y sequenc e probably originates from a retrotranscription event of a coding sequence mapped to chromosome 3 [33,34]. Furthermore, as opposed to a number of varying Y-specific fragments, only one or two autosomal TaqI fragments of apparent uniform intensity are detected by 49a and 49f, respectively. This implies that the copy number increase detected on the Y chromosome occurred only after the transfer of the sequence from the autosome. There is no reason to assume that this region would remain static and be free from further gene an~plification events. Despite these findings, the ability of 49a/f to detect numerous Y-specifc haplotypes has lent itself to use in regional population studies [22,23.,30-32], and it has also confirmed the Negroid/Eurasian dichotomy [22,23"]. The most com,incing demonstration of this African/nonAfrican split was shown using genetic distance measurements based on 49a/TaqI haplotype (Ht) frequencies [23"], which might be taken as support for the 'out of Africa' model. On the other hand, African populations have been shown to be far more homogeneous than Caucasoid populations, with TaqI Ht4 frequencies of 0.68 in western and central African Negroids [22], and 0.39-0.86 in southern African Negroids [23"]. This contrasts with mtDNA studies where the greatest within-group variation occurred in African populations [1,2",35,36]. The discrepancy may be partly explained by the common African practice of polygamy, the effect of which should not be underestimated [37]. It is likely that the nonrandom matings resulting from polygamous marriages could cause extreme shifts in gene frequencies. There is also evidence from 49a/TaqI Ht frequencies to suggest a division within the Caucasoid group, as discussed in the following section. While Europeans are distinctive because of a high frequency of Htl5 and
The Y chromosome as a tool for studying human evolution Spurdle, Jenkins 489 Htl2 [22,23"](A Novelletto, personal communication), the situation is different for Indian and Jewish populations. Ht14 was found to be most common in Asiatic Indians from three locations in India [31], but Ht7, Ht8, Ht11 and sometimes Ht24 are most common in South African Asiatic Indian and Jewish populations [23"], and in Ashkenazi and Sephardic Jews sampled in Israel and Tunisia (O Semino, AS Santachiara Benerecetti, personal communication). The 49a/f probes have been used to establish a genealogy of the Y chromosome, based on the successive loss of Taql sites by CpG methylation [30,31,38]. In this way, a haplotype found in the Pygmy population has been predicted to be ancestral. The involvement of rearrangements in the generation of the 49a polymorphism does, however, seriously question the validity of such an approach, and the conclusions drawn therefrom. Physical mapping of the area may lead to a better understanding of how the polymorphism is generated, and might allow for the development of systems, using techniques such as PCR and sequencing, to distinguish between hapiotypes that are presently unresolvable.
Other Y-specific polymorphisms The two allele deletion/insertion polymorphism detected by pl2f 2 has been shown to clearly distinguish Africans from non-Africans [20,39], but has not been used in extensive evolutionary studies. Research on the pseudoautosomal boundary region and the MspI polymorphism XY275 have proven to be more useful [25,26,40°]. Strong linkage disequilibrium was observed between the pseudoautosomal XY275 polymorphism and the Y boundary [25]. The alleles of the XY275 locus are termed high and low, signifying absence and presence of the MspI site, respectively [25]. Fixation of the high allele occurred in all groups with the exception of two African populations, suggesting that a single class of Y chromosome migrated out of Africa [25]. In contrast, a recent study has shown the Caucasoid Asiatic Indian population of South Africa to possess the 'African-specific' low allele [41"], intimating that more than one class of Y chromosome gave rise to the present.day non-African population. Interestingly, a study of three hypervariable loci detected by PFGE [21] has led to the proposal that most European and Asian men are descended from one of two males. The haplotypes defined by the three loci encompassed 12 probe/enzyme combinations, including the HindlII/pY~xl polymorphism. Two groups were distinguished in this way - group 1 consisting of Caucasoids only, and group 2 containing Asians (including Orientals) and Caucasoids. The pYotl/HindlII ' + ' allele occurred infrequently (0.05) in group 1, but in all members of group 2, with an overall frequency of 0.41. The latter polymorphism has also been studied in Egyptians, Italians and Sardinians, as well as in a British sample (A NoveUetto, personal communication). The ' + ' allele occurs at much higher frequencies (0.75-0.87) in all but
the British sample (0.33), suggesting that the Egyptian, Italian and Sardinian populations are largely comprised of 'group 2' individuals. Furthermore, screening for the XY275 polymorphism in these populations showed the Y-associated low allele to be present in the Egyptian sample only, at a frequency of 0.09 (A Novelletto, personal communication). This implies that at least three ancestral Y chromosomes existed in these populations. The hypervariable polymorphisms reported by Oakey and Tyler-Smith [21] have not yet been studied in Negroid populations, and research in this area may prove to be of significance in Y-specific human evolutionary Studies.
Conclusions The paucity of conventional polymorphism on the Y chromosome has hindered the use of the Y chromosome in the study of human evolution. A concerted collaborative effort will be required if this chromosome is to contribute to our understanding of human origins and evolution to anything like the same extent that nuclear and mitochondrial DNA variation has done. Y chromosome polymorphisms do however reveal evolutionary patterns strikingly different from those demonstrated by nuclear and mitochondrial DNA studies. Such differences may be the result of the unique pattern of paternal gene flow, complicated by cultural practices accentuating male/female behavioural differences. Polygamy and geographical mobility are two obvious factors enhancing this phenomenon. The logic of approaches to preceding evolutionary studies would thus be invalid for corresponding, and possibly complementary, Y chromosomal studies.
Acknowledgements This review has benefited from generous personal communications from a number of colleagues. We would like to extend our gratitude to D Bailey, M Hammer, M Jobiing, A Novelletto, AS Santachiara Benerecetti, O Semino, K Taylor, J Wolfe and Z Ulinowski for unpublished data and critical comments on this manuscript.
References and recommended reading Papers of particular interest, published within the annual period of review, have been highlighted as: • of special interest •, of outstanding interest CANN RE, STONEIrdNG M, WILSON AC: Mitochondrial DNA and Human Evolution. Nature 1987, 325:31-36. 2. •.
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490
Mammalian g e n e t i c s STRINGER CB, ANDREWS P: Genetic and Fossil Evidence for the Origin of Modern Humans. Science 1988, 239:1263-1268. WOLPOFF MH: Multiregional Evolution: the Fossil Alternative to Eden. In The Human Revolution. Edited by Mellars PA, Stringer CB. Edinburgh: University of Edinburgh Press; 1989:62-108. CAVALLI-SFORZA LL, EDWARDS AWF: Phylogenetic Analysis-models and Estimation Procedures. Am J Hum Genet 1967, 19:233-257. PIAZZA A, SGARAMELLA-ZONTAL, GLUCIOtAN P, CAVALLI-SFORZA LI= The Fifth Histocompatibility Workshop Gene Frequency Data: a Phlogenetic Analysis. Tissue Antigens 1975, 5:445-463. WAINSCOAT JS, HiLL AVS, BOYCE AL, FLINT J, HERNANDEZ M, THEIN SL, OLD JR, LYNCHJR, FALUSIAG, WEATHERALLDJ, CLEGG JB: Evolutionary Relationships of Human Populations from an Analysis of Nuclear DNA Polymorphisms. Nature 1986, 319:491-493. BOWCOCK AM, Bucci C, HEBERT JM, KIDD JR, KIDD KK, FRIDLANDERJS, CAVALL/-SFORZALL: Study of 47 DNA Markers in Five Populations from Four Continents. Gene Geogr 1987, 1:47-64. 9.
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A report of the cloning of the X-encoded amelogenin gene and the amelogenin-like sequence on the Y chromosome. Evidence is presented for an im,ersion event during the evolution of the Y chromosome. This inversion is possibly the same event postulated to have occurred during primate evolution from studies on the human X-linked steroid sulphatase gene and its Y-encoded pseudogene. 18. •
BARDONIB, ZUFFARDIO, Gulm S, BALLABIOA, SIMI P, CAVALLX P, GPdMOLDIMG, FRACO,RO M, CAMERINOG: A Deletion Map of the Human Yql I Region: Implications for the Evolution of the Y Chromosome and Tentative Mapping of a Locus Involved in Spermatogenesis. Genomics 1991, 11:443-451. A comparison of sequence order in the X/Y homologous regions of Yqll and Xp22.3 suggests at least three physically and temporally distinct rearrangements. DEGOUISR, HARDEUNJ-P, DEXqLLIERSJ, CLAVERIEJ-M, COMPAINS, WUNDERLEV, MILL&SSEAUP, DE PASLIERD, COHEN D, CATERINA D, ~'r aL: The Candidate Gene for the X-linked Kallmann Syndrome Encodes a Protein Related to Adhesion Molecules. Cell 1991, 67:423-435. The X-linked Kallman gene is shown to have a Ydinked pseudogene. 19. •
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CASANOVAM, LEROY P, BOUCEKK/NEC, WEISSENBACHJ, BISHOP C, FELLOUSM, PURRELO M, FtOPd G, S1NISCALCOM: A Human Y-linked DNA Polymorphism and its Potential for Estimating Genetic and Evolutionary Distance. Science 1985, 230:1403-1406.
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23. •
SPURDLEAB, JENKINS T: Y Chromosome Probe p49a Detects Complex Pvull Haplotypes and Many New Taql Haplotypes in Southern African Populations. Am J Hum Genet 1992, 50:107-127. A study of 49a/Taql haplotype frequencies in 831 Southern African individuals reveals an African/non-African split. Rearrangement processes are implicated in the generation of the 49a/Taql polymorphism. 24.
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CSARLRSWORTHB: The Evolution of Sex Chromosomes. Sci. A ence 1991, 251:1030-1033. description of the evolutionary paths giving rise to the present-day sex chromosomes. 14.
ELLXSNA: The Human Y Chromosome. Semin Dev Biol 1991, 2:2331-240. A general review of the Y chromosome, including a description of the evolution of the Y chromosome.
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WEISSENBACHJ: Single Copy DNA Sequences Specific for the 15.
YEN PH, MARSH B, ALLEN E, TSAI SP, ELLISON J, CONNOLLY L, NEISWANGERK, SHAPIRO LJ: The Human X-linked Steroid Sulphatase Gene and a Y-encoded Pseudogene: Evidence for an Inversion of the Y Chromosome During Primate Evolution. Cell 1988, 55:1123-1135.
Human Y Chromosome. Nature 1983, 303:831--832. 28.
NGO KY, VERGNAUDG, JOHNSSON C, LUCOTTE G, WEISSENBACH J: A DNA Probe Detecting Multiple Haplotypes of the Human Y Chromosome. Am J Hum Genet 1986, 38:407-418.
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BREGA A, TORRONI A, SEMINO O, MACCIONE L, CASANOVAM, SCOZZAm R, FELLOUS M, SANTACHIARABENERECETTI AS: The pl2f2/TaqI Y-specific Polymorphism in Three Groups of Italians and in a Sample of senegalese. Gene Geogr 1987, 1:201-206.
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BREGAA, SCOZZARI R, MACCIONE L, IODICE C, WALLACE DC, B1ANCO I, CAO A, SANTACHIARABENERECETTIAS: Mitochondrial DNA Polymorphisms in Italy. I. Population Data from Sardinia and Rome. A n n H u m Genet 1986, 50:327-338.
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40. ELLIS NA: Erratum. Am J H u m Genet 1991, 49:908. • The previously named XY274 polymorphism is in fact a G to T transversion within a MspI site, occurring 275bp from the boundary, and is renamed XY275. 41. •
SPURDLEA, RAMSAYM, JENKINS T: The Y-associated XY275 L o w Allele is not Restricted to Indigenous African Peoples. Am J H u m Genet 1992, in press. The XY275 low allele occurs in association with the Y chromosome in the Caucasoid South African Asiatic Indian population, suggesting that more than one class of Y chromosome gave rise to the present-day non-African population.
AB Spurdle, T Jenkins, Department of Human Genetics, South African Institute for Medical Research, PO Box 1038, Johannesburg 2000, South Africa.
491
Current Opinion in Genetics and Development 1992, 2:487-491
Introduction Scientists have long been fascinated by studies of the origin and more recent evolution of mankind. Paleoanthropological research has led to two opposing theories of origin, popularly known as the 'out of Africa' and multiregional continuum models. The 'out of Africa' hypothesis proposes that modem humans evolved in Africa, and subsequendy dispersed throughout Europe and Asia, replacing all other hominids [1,2oo]. As an extension of this theory, distinction at the genetic level has been implicated in the lack of interbreeding between the archaic humans occupying Europe and Asia, and the invading African ancestor [3]. The multiregional continuum model postulates that modem humans evolved gradually and simultaneously from local forms of H o m o erectus which had themselves spread from Africa to Europe and Asia [4]; the unity of the species is presumed to have been maintained by gene exchange between the isolates. Research in the field of human genetic variation has ushered in a new era in evolutionary research, and various molecular studies have been undertaken in an attempt to resolve uncertainties resulting from different interpretations of paleoanthropological data. These studies range from the pioneering serogenetic [5] and human leukocyte antigen-complex (HLA) [6] studies to DNAbased restriction fragment length polymorphism (RFLP) analysis of beta-globin markers [7], mitochondrial (mt) DNA [1] and nuclear gene markers [8,9,10oo]. More recently, a comprehensive study invoMng DNA sequencing of the mt.DNA D-loop region has been presented [2°°]. The molecular approach to evolutionary studies is based on the assumption that if modem man arose in Africa,
then African and non-African humans would be most geneticaUy distinct, and African populations would exhibit more within-group genetic variation than the non-African populations that stemmed from an African migration. With little exception, the molecular data confirm the African/non-African split, in support of the 'out of Africa' model. Many researchers have recognized the potential of Y chromosome population and evolutionary studies for providing a record of male-specific gene flow and human evolution, and to thus complement or expand studies using mtDNA or nuclear markers. Unfortunately, the role of the Y chromosome in this area has been limited, not by inadequate effort, but by the singular lack of polymorphism discovered on this chromosome to date. These findings are especially troubling since interpopulation variation differences can only be truly evaluated in light of within-group variation, and it will be di/~cult to make progress and to draw accurate conclusions of an evolutionary nature as long as we are limited by the low levels of Y-specific variation. This review describes current findings on the level of Y chromosome polymorphism, and also details results from Y chromosome population/evolutionary studies using several different Y-specific polymorphic loci.
The paucity of Y chromosome polymorphism Several studies have been undertaken to search for conventional RFLPs on theY chromosome [11, 12] (A Spur-
Abbreviations HLA--human leukocyteantigen-complex;Ht--haplotype; rnt--mitochondrial;PFGE~pulsed-fieldgel electrophoresis; RFLP--restrictionfragment length polyrnnorphisrn. (~ Current Biology Ltd ISSN 0959-437X
487
488 Mammaliangenetics die, T Jenkins, unpublished data; M Jobling, personal communication). Despite these systematic searches, a paucity of polymorphism exists, with reported levels of polymorphism as low as < 1/18000 nucleotides [11] and < 1/46515 nucleotides [12]. This lack of variation is not confined to nucleotide changes occurring within restriction endonuclease sites. Studies on two Y-derived CA repeats have not revealed any polymorphism in 20 Caucasian/Asian males (Z Ulinowski, D Bailey, K Taylor, J Wolfe, personal conmmnication). The repeats also appear to occur less frequently, with positive signals for 5% of Y cosmids, as opposed to 20% of cosmids derived from the long arm of chromosome 9 (9q). In addition, sequencing of the Y chromosome has revealed a very low level of nucleotide diversity, although somewhat higher than estimates based on RFLP studies (M Hammer, personal communication). The implication is that many kilobases of each Y chromosome would need to be sequenced to match the information revealed by mtDNA D-loop sequences used in published evolutionary studies [2"']. This dearth of polymorphism is unexpected in view of theories on the origin of the Y chromosome (see [13%14"] for a review). The proto-Y chromosome is believed to have evolved from a homologous proto-X chromosome, and with the exception of the genes involved in sex determination and the present region of homology between the sex chromosomes, was prone to rearrangement processes and loss/inactivation of genes [15,16,17"-19.]. The Y chromosome was presumably also free to accumulate satellite sequences and noncoding retrotransposed elements originating from autosomes, possibly as a response to selection for a chromosome size that would be appropriate for efficient meiotic segregation [18.]. Despite this plethora of non-coding sequences, simple sequence polymorphism is rare, and most of the reported Y-specific polymorphism is generated, at least in part, by rearrangement processes [20-22,23"]. Malaspina et at [12] have proposed several explanations for the low frequency of polymorphism on the Y chromosome. One suggestion is that the mechanisms protecting the Y chromosome from recombination may simultaneously protect it from mutagenesis, but the role of recombination in maintaining genetic variation is considered more important [12]. The latter explanation arises from the postulate by Clark [24] that Y chromosome polymorphism is unlikely to be maintained by natural selection. It is possible that insufficient time has elapsed since the origin of the present-day Y chromosome to allow for the accumulation of significant polymorphism. Indeed, sequencing studies of the pseudoautosomal boundary region [25,26] show that the Y boundary exhibits less variation than the X boundary, suggesting that it has evolved more recently. However, a survey for long-range Y-specific polymorphism using pulsed-field gel electrophoresis (PFGE) has identified several novel hypervariable blocks (M Jobling, personal communication), contrasting with the results from RFLP screening. These findings suggest that such large scale
polymorphism is generated at a higher rate than simple sequence polymorphism.
The value of the Y-specific probes 49a and 49f Y chromosome probes 49a and 49f are different subclones of cosmid 49 [27], and both detect about 15 Y-specific TaqI bands corresponding to a low copy number sequence [28]. At least eight of these bands have been shown to be present, absent or variable in length [22,23",28-31]. Each variable band was originally considered to represent an independent locus, and the TaqI RFLPs were proposed to result from point mutations only [28]. Recent reports of co-inherited 'alleles' of the A, D and F series [22,23.] have led, however, to the realization that duplication processes cannot be excluded as a mechanism for the generation of at least part of the polymorphism. Thus fragments that appear to be identical may not necessarily originate from the same piece of DNA, and in some cases may represent more than one copy of a duplicated 'locus'. In retrospect, the existence of rearrangements should not be unexpected in view of the origin and nature of the repeat sequences detected by 49a/f. The Y sequenc e probably originates from a retrotranscription event of a coding sequence mapped to chromosome 3 [33,34]. Furthermore, as opposed to a number of varying Y-specific fragments, only one or two autosomal TaqI fragments of apparent uniform intensity are detected by 49a and 49f, respectively. This implies that the copy number increase detected on the Y chromosome occurred only after the transfer of the sequence from the autosome. There is no reason to assume that this region would remain static and be free from further gene an~plification events. Despite these findings, the ability of 49a/f to detect numerous Y-specifc haplotypes has lent itself to use in regional population studies [22,23.,30-32], and it has also confirmed the Negroid/Eurasian dichotomy [22,23"]. The most com,incing demonstration of this African/nonAfrican split was shown using genetic distance measurements based on 49a/TaqI haplotype (Ht) frequencies [23"], which might be taken as support for the 'out of Africa' model. On the other hand, African populations have been shown to be far more homogeneous than Caucasoid populations, with TaqI Ht4 frequencies of 0.68 in western and central African Negroids [22], and 0.39-0.86 in southern African Negroids [23"]. This contrasts with mtDNA studies where the greatest within-group variation occurred in African populations [1,2",35,36]. The discrepancy may be partly explained by the common African practice of polygamy, the effect of which should not be underestimated [37]. It is likely that the nonrandom matings resulting from polygamous marriages could cause extreme shifts in gene frequencies. There is also evidence from 49a/TaqI Ht frequencies to suggest a division within the Caucasoid group, as discussed in the following section. While Europeans are distinctive because of a high frequency of Htl5 and
The Y chromosome as a tool for studying human evolution Spurdle, Jenkins 489 Htl2 [22,23"](A Novelletto, personal communication), the situation is different for Indian and Jewish populations. Ht14 was found to be most common in Asiatic Indians from three locations in India [31], but Ht7, Ht8, Ht11 and sometimes Ht24 are most common in South African Asiatic Indian and Jewish populations [23"], and in Ashkenazi and Sephardic Jews sampled in Israel and Tunisia (O Semino, AS Santachiara Benerecetti, personal communication). The 49a/f probes have been used to establish a genealogy of the Y chromosome, based on the successive loss of Taql sites by CpG methylation [30,31,38]. In this way, a haplotype found in the Pygmy population has been predicted to be ancestral. The involvement of rearrangements in the generation of the 49a polymorphism does, however, seriously question the validity of such an approach, and the conclusions drawn therefrom. Physical mapping of the area may lead to a better understanding of how the polymorphism is generated, and might allow for the development of systems, using techniques such as PCR and sequencing, to distinguish between hapiotypes that are presently unresolvable.
Other Y-specific polymorphisms The two allele deletion/insertion polymorphism detected by pl2f 2 has been shown to clearly distinguish Africans from non-Africans [20,39], but has not been used in extensive evolutionary studies. Research on the pseudoautosomal boundary region and the MspI polymorphism XY275 have proven to be more useful [25,26,40°]. Strong linkage disequilibrium was observed between the pseudoautosomal XY275 polymorphism and the Y boundary [25]. The alleles of the XY275 locus are termed high and low, signifying absence and presence of the MspI site, respectively [25]. Fixation of the high allele occurred in all groups with the exception of two African populations, suggesting that a single class of Y chromosome migrated out of Africa [25]. In contrast, a recent study has shown the Caucasoid Asiatic Indian population of South Africa to possess the 'African-specific' low allele [41"], intimating that more than one class of Y chromosome gave rise to the present.day non-African population. Interestingly, a study of three hypervariable loci detected by PFGE [21] has led to the proposal that most European and Asian men are descended from one of two males. The haplotypes defined by the three loci encompassed 12 probe/enzyme combinations, including the HindlII/pY~xl polymorphism. Two groups were distinguished in this way - group 1 consisting of Caucasoids only, and group 2 containing Asians (including Orientals) and Caucasoids. The pYotl/HindlII ' + ' allele occurred infrequently (0.05) in group 1, but in all members of group 2, with an overall frequency of 0.41. The latter polymorphism has also been studied in Egyptians, Italians and Sardinians, as well as in a British sample (A NoveUetto, personal communication). The ' + ' allele occurs at much higher frequencies (0.75-0.87) in all but
the British sample (0.33), suggesting that the Egyptian, Italian and Sardinian populations are largely comprised of 'group 2' individuals. Furthermore, screening for the XY275 polymorphism in these populations showed the Y-associated low allele to be present in the Egyptian sample only, at a frequency of 0.09 (A Novelletto, personal communication). This implies that at least three ancestral Y chromosomes existed in these populations. The hypervariable polymorphisms reported by Oakey and Tyler-Smith [21] have not yet been studied in Negroid populations, and research in this area may prove to be of significance in Y-specific human evolutionary Studies.
Conclusions The paucity of conventional polymorphism on the Y chromosome has hindered the use of the Y chromosome in the study of human evolution. A concerted collaborative effort will be required if this chromosome is to contribute to our understanding of human origins and evolution to anything like the same extent that nuclear and mitochondrial DNA variation has done. Y chromosome polymorphisms do however reveal evolutionary patterns strikingly different from those demonstrated by nuclear and mitochondrial DNA studies. Such differences may be the result of the unique pattern of paternal gene flow, complicated by cultural practices accentuating male/female behavioural differences. Polygamy and geographical mobility are two obvious factors enhancing this phenomenon. The logic of approaches to preceding evolutionary studies would thus be invalid for corresponding, and possibly complementary, Y chromosomal studies.
Acknowledgements This review has benefited from generous personal communications from a number of colleagues. We would like to extend our gratitude to D Bailey, M Hammer, M Jobiing, A Novelletto, AS Santachiara Benerecetti, O Semino, K Taylor, J Wolfe and Z Ulinowski for unpublished data and critical comments on this manuscript.
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SPURDLEA, RAMSAYM, JENKINS T: The Y-associated XY275 L o w Allele is not Restricted to Indigenous African Peoples. Am J H u m Genet 1992, in press. The XY275 low allele occurs in association with the Y chromosome in the Caucasoid South African Asiatic Indian population, suggesting that more than one class of Y chromosome gave rise to the present-day non-African population.
AB Spurdle, T Jenkins, Department of Human Genetics, South African Institute for Medical Research, PO Box 1038, Johannesburg 2000, South Africa.
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